Phylogenetic Inference

Common ancestry is one of the pillars of Darwin’s theory of evolution. Today, the Tree of Life, which represents how all life is genealogically related, is often thought of as an essential component in the foundations of biological systematics and so therefore of evolutionary theory – and perhaps all of biology itself. It is an iconic representation in biology and even penetrates into popular culture.

Abstract: Under traditional Jewish Law (halacha), assessment of human reproductive cloning (HRC) has been formulated along four lines of inquiry, which I discussed in Part I of this paper. Therein I also analyze five relevant doctrines of Talmudic Law, concluding that under with a risk-benefit analysis HRC fails to fulfill the obligation ‘to be fruitful and multiply’ and should be strictly prohibited. Here, I review of the topic from an exigetical Biblical and Kabbalistic perspective, beginning with exploring comments of the (...) Ramban (Nachmanides) which suggest Kabbalistic insights very much in keeping with current biology. In this Part II of the paper, I expand and annotate statements of the Ramban on the interrelationship of the reproductive faculties of an organism and its soul by examining the development of the spiritual states of plant, animal and human and noting the commensurate evolution with its reproductive facilities. Speculating that the reproductive mechanism of each species is indelibly related to its soul-state, I suggest that interfering with human sexual reproduction by HRC has the same effect the Ramban argues is the result of Kilayim (interbreeding), i.e., wrecking havoc with the Universe. In Part III, I postulate a biologic explanation for warnings found in the Golemic Literature and suggest that these allude to the importance of maintaining human genetic diversity through sexual reproduction. The conclusions I reached after evaluating the propriety of HRC under a Kabbalistic/metaphysical index comports with those I reached using a traditional legal /halachic inquiry in Part I. Thus, both systems arrive at the conclusion that HRC is in violation of the divine and natural order and constitute a distinct biological threat to the survival of the human species, a conclusions in accord with current scientific thinking. (shrink)

This paper poses a problem for traditional phylogenetics: The identity of organisms that reproduce through fission can be understood in several different ways. This prompts questions about how to differentiate parent organisms from their offspring, making vertical gene transfer unclear. Differentiating between parents and offspring stems from what I call the identity problem. How the problem is resolved has implications for phylogenetic groupings. If the identity of a particular asexual organism persists through fission, the vertical lineage on a phylogenetic tree (...) will split differently than if the identity of an organism does not survive the fission process. (shrink)

The present work analyzes the controversy within biological systematics regarding the status of cladistics. The use of the parsimony method for phylogenetic reconstruction has been defended by appealing to a methodological principle of simplicity, as well as to empirical principles that external to systematics. I propose new kind of approach, which consists in considering it an empirical theory, thus justifying its application by its empirical success. To defend this point, a formal structuralist reconstruction of cladistics will be provided, which will (...) help clarify what its central empirical statements are. At the same time, I show how these principles have been used to test that theory using experimental phylogenies. (shrink)

In this article, I examine the issue of the alleged circularity in the determination of homologies within cladistic analysis. More specifically, I focus on the claims made by the proponents of the dynamic homology approach, regarding the distinction between primary and secondary homology. This distinction is sometimes invoked to dissolve the circularity issue, by upholding that characters in a cladistic data matrix have to be only primarily homologous, and thus can be determined independently of phylogenetic hypotheses, by using the classical (...) Owenian criteria or via multiple sequence alignment. However, since in the dynamic approach, sequence data can be analyzed without being pre-aligned, proponents have claimed that the distinction between primary and secondary homology has no place within cladistics. I will argue that this is not the case, since cladistic practice within the dynamic framework does presuppose primary homology statements at a higher level. (shrink)

Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, if (...) at all, does genealogical discordance challenge, modify, or revise how we conceive of species? (2) How has growing appreciation of genealogical discordance impacted scientific practice? Of systematics in particular? (3) How do lineages at different levels diverge and diversify? All told, genealogical discordance enriches and complicates our taxonomic ontology, as well as the practice of reconstructing phylogenies. This presents both challenges and opportunities for the study of divergence and diversification. (shrink)

Philosophers of biology have worked extensively on how we ought best to interpret the probabilities which arise throughout evolutionary theory. In spite of this substantial work, however, much of the debate has remained persistently intractable. I offer the example of Bayesian models of divergence time estimation as a case study in how we might bring further resources from the biological literature to bear on these debates. These models offer us an example in which a number of different sources of uncertainty (...) are combined to produce an estimate for a complex, unobservable quantity. These models have been carefully analyzed in recent biological work, which has determined the relationship between these sources of uncertainty, both quantitatively and qualitatively. I suggest here that this case shows us the limitations of univocal analyses of probability in evolution, as well as the simple dichotomy between “subjective” and “objective” probabilities, and I conclude by gesturing toward ways in which we might introduce more sophisticated interpretive taxonomies of probability as a path toward advancing debates on probability in the life sciences. (shrink)

© The Author 2017. Published by Oxford University Press on behalf of The Scots Philosophical Association and the University of St Andrews. All rights reserved. For permissions, please e-mail: [email protected] A. Richards offers a comprehensive introduction to biological classification: ‘the comparison and grouping of organisms, the naming of these groups, the theoretical basis for grouping, and the philosophical foundations for systems of grouping’. This book functions as an introduction to philosophy for biologists, an introduction to biology for philosophers and an (...) introduction to the history of both suitable for a more general audience.In the first chapter, he considers the results of folk and ethno-taxonomy, and related studies in cognitive psychology and developmental linguistics. The results suggest that all humans classify hierarchically, and that there is some agreement between folk and ethno-taxonomy and scientific taxonomy. But, even with this agreement, there is still disagreement about the ‘naturalness’... (shrink)

ABSTRACT ‘Modus Darwin’ is the name given by Elliott Sober to a form of argument that he attributes to Darwin in the Origin of Species, and to subsequent evolutionary biologists who have reasoned in the same way. In short, the argument form goes: similarity, ergo common ancestry. In this article, I review and critique Sober’s analysis of Darwin’s reasoning. I argue that modus Darwin has serious limitations that make the argument form unsuitable for supporting Darwin’s conclusions, and that Darwin did (...) not reason in this way. (shrink)

Media reporters often announce that we are on the verge of bringing back the woolly mammoth, even while there is growing consensus among scientists that resurrecting the mammoth is unlikely. In fact, current “de-extinction” efforts are not designed to bring back a mammoth, but rather adaptations of the mammoth using close relatives. For example, Harvard scientists are working on creating an Asian elephant with the thick coat of a mammoth by merging mammoth and elephant DNA. But how should such creatures (...) be classified? Are they elephants, mammoths, or both? Answering these questions requires getting clear about the concept of reproduction. What I hope to show is that with an appropriate notion of reproduction—one for which I will argue—resurrecting a member of Mammuthus primigenius is a genuine possibility. (shrink)

A. W. F. Edwards is one of the most influential mathematical geneticists in the history of the discipline. One of the last students of R. A. Fisher, Edwards pioneered the statistical analysis of phylogeny in collaboration with L. L. Cavalli-Sforza, and helped establish Fisher's concept of likelihood as a standard of statistical and scientific inference. In this book, edited by philosopher of science Rasmus Grønfeldt Winther, Edwards's key papers are assembled alongside commentaries by leading scientists, discussing Edwards's influence on their (...) own research and on thinking in their field overall. In an extensive interview with Winther, Edwards offers his thoughts on his contributions, their legacy, and the context in which they emerged. This book is a resource both for anyone interested in the history and philosophy of genetics, statistics, and science, and for scientists seeking to develop new algorithmic and statistical methods for understanding the genetic relationships between and among species both extant and extinct. (shrink)

Here, I consider the recent application of phylogenetic methods in historical linguistics. After a preliminary survey of one such method, i.e. cladistic parsimony, I respond to two common criticisms of cultural phylogenies: that cultural artifacts cannot be modeled as tree-like because of borrowing across lineages, and that the mechanism of cultural change differs radically from that of biological evolution. I argue that while perhaps remains true for certain cultural artifacts, the nature of language may be such as to side-step this (...) objection. Moreover, I explore the possibility that cladistic parsimony can be justified even if is true by appealing to the inference pattern known among philosophers as ‘Inference to the Best Explanation’. (shrink)

Among philosophical analyses of Darwin’s Origin, a standard view says the theory presented there had no concrete observational consequences against which it might be checked. I challenge this idea with a new analysis of Darwin’s principal geographical distribution observations and how they connect to his common ancestry hypothesis.

The term “cladist” has distinct meanings in distinct contexts. Communication between philosophers, historians, and biologists has been hindered by different understandings of the term in various contexts. In this paper I trace historical and conceptual connections between several broadly distinct senses of the term “cladist”. I propose seven specific definitions that capture distinct contemporary uses. This serves to disambiguate some cases where the meaning is unclear, and will help resolve apparent disagreements that in fact result from conflicting understandings of the (...) term. (shrink)

Early nineteenth century systematists sought to describe what they called the Natural System or the Natural Classification. In the nineteenth century, there was no agreement about the basis of observed patterns of similarity between organisms. What did these systematists think they were doing, when they named taxa, proposed relationships between taxa, and arranged taxa into representational schemes? In this paper I explicate Charles Frederic Girard’s (1822–1895) theory and method of systematics. A student of Louis Agassiz, and subsequently (1850–1858) a collaborator (...) with Spencer Baird, Girard claimed that natural classificatory methods do not presuppose either a special creationist or an evolutionary theory of the natural world. The natural system, in Girard’s view, comprises three distinct ways in which organisms can be related to each other. Girard analyzed these relationships, and justified his classificatory methodology, by appeal to his embryological and physiological work. Girard offers an explicit theoretical answer to the question, what characters are evidence for natural classificatory hypotheses? I show that the challenge of simultaneously depicting the three distinct types of relationship led Girard to add a third dimension to his classificatory diagrams. (shrink)

While Bayesian methods have become very popular in phylogenetic systematics, the foundations of this approach remain controversial. The star-tree paradox in Bayesian phylogenetics refers to the phenomenon that a particular binary phylogenetic tree sometimes has a very high posterior probability even though a star tree generates the data. I argue that this phenomenon reveals an unattractive feature of the Bayesian approach to scientific inference and discuss two proposals for how to address the star-tree paradox. In particular, I defend the polytomy (...) prior as a solution of the paradox and argue that it is preferable to a data-size dependent branch lengths prior from a methodological perspective. However, while this reply dissolves the star-tree paradox, the general challenge to Bayesian confirmation theory remains unmet. (shrink)

This chapter explores the idea that phylogenetic diversity plays a unique role in underpinning conservation endeavour. The conservation of biodiversity is suffering from a rapid, unguided proliferation of metrics. Confusion is caused by the wide variety of contexts in which we make use of the idea of biodiversity. Characterisations of biodiversity range from all-variety-at-all-levels down to variety with respect to single variables relevant to very specific conservation contexts. Accepting biodiversity as the sum of a large number of individual measures results (...) in an empirically intractable framework. However, large-scale decisions cannot be based on biodiversity variables inferred from local conservation imperatives because the variables relevant to the many systems being compared would be incommensurate with one another. We therefore need some general conception of biodiversity that would make tractable such large-scale environmental decision-marking. We categorise the large array of strategies for the measurement of biodiversity into four broad groups for consideration as general measures of biodiversity. We compare common moral justifications for the conservation of biodiversity and conclude that some form of instrumental value is the most plausible justification for biodiversity conservation. Although this is often interpreted as a reliance on option value, we opt for a broadly consequentialist characterisation of biodiversity conservation. We conclude that the best justified general measure of biodiversity will be some form of phylogenetic diversity. (shrink)

William Whewell’s work on historical science has received some attention from historians and philosophers of science. Whewell’s own work on the history of German Gothic church architecture has been touched on within the context of the history of architecture. To a large extent these discussions have been conducted separately. I argue that Whewell intended his work on Gothic architecture as an attempt to (help) found a science of historical architecture, as an exemplar of historical science. I proceed by analyzing the (...) key features of Whewell’s philosophy of historical science. I then show how his architectural history exemplifies this philosophy. Finally, I show how Whewell’s philosophy of historical science matches some developments in a science (biological systematics) that, in the mid-to latenineteenth century, came to be reinterpreted as a historical science. I comment briefly on Whewell as a potential influence on nineteenth century biology and in particular on Darwin. (shrink)

I respond to the bad lot argument in the context of biological systematics. The response relies on the historical nature of biological systematics and on the availability of pattern explanations. The basic assumption of common descent enables systematic methodology to naturally generate candidate explanatory hypotheses. However, systematists face a related challenge in the issue of character analysis. Character analysis is the central problem for contemporary systematics, yet the general problem of which it is a case—what counts as evidence?—has not been (...) adequately discussed by proponents of inference to the best explanation. Facing this problem is the price of adopting abductive methods. I sketch an account of how systematists approach the problem of evidence. (shrink)

If asked to explain why the Golds’ treatment of other colors in Red Rising is wrong, it is tempting to say something like “they are all human beings, and it is wrong to treat humans in this way!” In this essay, I’ll argue that this simple answer is considerably complicated by the fact that the different colors might not be members of the same biological species, and it is in fact unclear whether any of them are the same species as (...) current humans. Explaining why exactly this is so will lead us to an exploration the long-running debate in biology and philosophy over what exactly it means for two organisms to be “members of the same species.” I’ll begin by discussing the biological essentialism of Aristotle and his followers, who held that an individual organism’s species was determined by essence. One can easily imagine that the Golds might find this attractive, since it would suggest that their “superior” mental and physical capacities made them a different (and probably “higher”) species of humanity than the other colors. Unfortunately for Aristotle, this turns out to be inconsistent with Charles Darwin’s account of evolution by natural selection. This development has led many modern biologists and philosophers of biology to conceptualize species not as an abstract “form” that serves to classify organisms, but rather as a concrete collection of organisms relatively close to each other in space and time. In contrast to biological essentialism, this view of “species as concrete individual” might seem to support the Reds’ claim to the “same species” as the Gold, since they are both part of the same overarching society. Next, I’ll consider how we might tell where one species “ends” and another one “begins.” As it turns out, biologists have many ways of answering his question, each of which makes different judgments about the species of Red Rising’s characters. So, for example, the “Biological Species Concept” bases judgements about species membership on the ability to produce fertile offspring. This concept is far from perfect, however, for reasons that Red Rising makes clear: it doesn’t deal clearly with cases where reproduction is possible but very difficult (a Red and a Gold having a child) or for organisms that do not reproduce sexually (such as Pinks). I’ll then explore a few prominent alternatives to BSC, including both genetically and ecologically based species concepts, and consider their consequences for the society of Red Rising. I’ll conclude by advocating for a “pluralism” about species membership, and will suggest that the people of Red Rising (as well as in the real world) should beware of basing arguments for moral or political equality on the all-too-slippery notion of “shared humanity.” Instead, they should focus on the qualities that make the lives of the individuals (regardless of their species) worth caring about, such as their shared desires to avoid suffering and to lead fulfilling, meaningful lives. (shrink)

John Wilkins and Malte Ebach respond to the dismissal of classification as something we need not concern ourselves with because it is, as Ernest Rutherford suggested, mere ‘‘stamp collecting.’’ They contend that classification is neither derivative of explanation or of hypothesis-making but is necessarily prior and prerequisite to it. Classification comes first and causal explanations are dependent upon it. As such it is an important (but neglected) area of philosophical study. Wilkins and Ebach reject Norwood Russell Hanson’s thesis that classification (...) relies on observation that is theory-laden and deny the need for aetiological assumptions and historical reconstruction to justify its arrangement. What they offer instead is a significant (albeit controversial) contribution to the philosophical literature on classification, a pre-theoretic natural classification based on the observation of patterns in data of ready-made phenomena. Their notion of ready-made phenomena rests on a conception of tacit knowledge or know-how. This is evident in their distinction between strong Theory-dependence and na ̈ıve theory-dependence. Their small t-theory-dependence permits patterns of observation that facilitate know-how but does not rely on a domain-specific explanatory theory of their aetiology. Wilkins and Ebach suggest classification differs from theory building in that it is passive (whereas theory building is active). Classification is possible just because it does not require the sieve of theory to capture classes that are ‘‘handed to you by your cognitive dispositions and the data that you observe’’ (p. 18). Finding regularities sans-theory is just something we do and can do without any prior theory about the underlying causes or origins of the resultant regularities. Luke Howard’s classification of clouds serves as an exemplar of a passive, theory-free classification system and the periodic table and the DSM help to illustrate this type of non-aetiological patterning. A recurrent theme is the nature of naturalness. For Wilkins and Ebach, the conception of naturalness is not one that is based on the generation or discovery of natural kind categories popular in both the traditional metaphysics of Mill and Wittgenstein as well as updated notions within philosophy of biology such as Boyd’s Homeostatic Property Cluster kinds. Instead, Wilkins and Ebach define the naturalness of classification as the falling into hierarchical patterns, aligning the search for natural arrangement with the aim of systematics, and as something that is grounded in a cognitive task or activity. However, they leave the question of realism v. antirealism open. ‘‘In natural classification...we must have real relations no matter how we might interpret ‘real’’’ (p. 70). There is tension with regard to their ontological commitments as they vacillate between constructive, operationalist, and realist approaches. Wilkins and Ebach initially define real as that which is causal and important (pp. 70–71), and later as that which ‘‘depends in no way upon a mind or observer’’ (p. 122). This makes their claim that there was ‘‘no real theory involved [in the pre-Darwinian classifications of Jussieu and Adanson]’’ (p. 64) difficult to interpret. Cont’d……. (shrink)

Darwin claims in the Origin that similarity is evidence for common ancestry, but that adaptive similarities are ‘almost valueless’ as evidence. This second claim seems reasonable for some adaptive similarities but not for others. Here we clarify and evaluate these and related matters by using the law of likelihood as an analytic tool and by considering mathematical models of three evolutionary processes: directional selection, stabilizing selection, and drift. Our results apply both to Darwin’s theory of evolution and to modern evolutionary (...) biology. 1 Introduction2 The Likelihood Framework3 A Sufficient Condition for a Similarity to Favour Common Ancestry over Separate Ancestry4 The 1/p Criterion and Its Limitations5 Directional Selection versus Drift6 Stabilizing Selection versus Drift7 Going beyond Two Taxa8 ConclusionsAppendix. (shrink)

From the 1960s, mathematical and computational tools have been developed to arrive at human population trees from various kinds of serological and molecular data. Focusing on the work of the Italian-born population geneticist Luigi Luca Cavalli-Sforza, I follow the practices of tree-building and mapping from the early blood-group studies to the current genetic admixture research. I argue that the visual language of the tree is paralleled in the narrative of the human diasporas, and I show how the tree was actually (...) mapped onto the surface of the earth. This visual and textual structure is mirrored in the liberal discourse of unity in diversity that has been criticized as running counter to the socio-political effects of human population genetics. From this perspective, one may ask how far the phylogenetic diagram in its various forms is a manifestation of the physics of power that according to Michel Foucault consists in mechanisms that analyse distributions, movements, series, combinations, and that uses instruments to render visible, to register, to differentiate and to compare. It is one among other disciplinary technologies that ensure the ordering of human diversity. In the case of intra-human phylogenetic trees, population samples and labels are one issue. Another is that the separated branches seem to show groups of people, who have in reality been interacting and converging, as isolated. Often based on so-called isolated peoples, molecular tree diagrams freeze a hierarchical kinship system that is meant to represent a state before the great historical population movements. (shrink)

Historical sciences like evolutionary biology reconstruct past events by using the traces that the past has bequeathed to the present. Markov chain theory entails that the passage of time reduces the amount of information that the present provides about the past. Here we use a Moran process framework to show that some evolutionary processes destroy information faster than others. Our results connect with Darwin’s principle that adaptive similarities provide scant evidence of common ancestry whereas neutral and deleterious similarities do better. (...) We also describe how the branching in phylogenetic trees affects the information that the present supplies about the past. (shrink)

The project of this paper is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial—or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in a trivial way, their interpretation (...) is tied to foundational conceptual questions at the heart of systematics—questions whose answers are hotly disputed. I have previously argued that widely shared ideas about the meaning and interpretation of phylogenetic trees are inconsistent with species concepts other than some genealogical version of a phylogenetic species concept (Velasco 2008). Here I rely on a similar approach and concentrate on the implications of the necessary conditions underlying the inferences that we make using phylogenetic trees. I argue that common practices for the interpretation and use of trees are in conflict and that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. This is true regardless of whether the tips of the trees are themselves populations, or are species or higher taxa. Although this conclusion might be paired naturally with a view that species must be monophyletic groups, this population-centric view of trees is independent of that view of species. If we still want to have species that are paraphyletic groups of populations, this is permissible as long as we also do not treat species as the units of phylogeny. This population-centric view opposes a species-centric view of phylogeny and might be called a “rank-free” approach since it entails that we do not need to determine which groups are species (which is partly a ranking question) in order to build a tree. This conclusion and the argument for it are meant to be consistent with, but not require, acceptance of the conclusions of Velasco (2008) regarding species. (shrink)

Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining the prior probabilities of phylogenetic trees by means of the Principal (...) Principle. In particular, I discuss a proposal due to Velasco (Biol Philos 23:455–473, 2008) of assigning prior probabilities to tree topologies based on the Yule process. By invoking the Principal Principle I argue that prior probabilities of tree topologies should rather be assigned a weighted mixture of probability distributions based on Pinelis’ (P Roy Soc Lond B Bio 270:1425–1431, 2003) multi-rate branching process including both the Yule distribution and the uniform distribution. However, I argue that this solves the problem of the priors of phylogenetic trees only in a weak form. (shrink)

A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular tree-based methods such as maximum parsimony and maximum likelihood face a serious problem—if we judge networks by (...) fit to data alone, networks that have lateral branches will always fit the data at least as well as any network that restricts itself to vertical branches. This is analogous to the well-studied problem of overfitting data in the curve-fitting problem. Analogous problems often have analogous solutions and we propose to treat network inference as a case of model selection and use the Akaike Information Criterion (AIC). Strictly tree-like networks are more parsimonious than those that postulate lateral as well as vertical branches. This leads to the conclusion that we should not always infer LGT events whenever it would improve our fit-to-data, but should do so only when the improved fit is larger than the penalty for adding extra lateral branches. (shrink)

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the (...) prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction into a thing . The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs. (shrink)

‘‘Adaptive radiation’’ is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making ‘‘adaptive radiation’’ so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny-based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts to shoehorn the (...) results of these techniques into categorical ‘‘adaptive radiation: yes/no’’ schemes lead to reification, in which arbitrary quantitative thresholds are regarded as real. Our account of the life cycle of metaphors in science suggests that it is time to exchange the spent metaphor for new concepts that better represent the full range of diversity, disparity, and speciation rate across all of life. (shrink)

I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.

Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different methods (...) of assigning prior probabilities to trees. I argue that priors need to be derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and about macroevolutionary processes more generally. (shrink)

In a series of articles, Rieppel (2005, Biol. Philos. 20:465–487; 2006a, Cladistics 22:186–197; 2006b, Systematist 26:5–9), Keller et al. (2003, Bot. Rev. 69:93–110), and Nixon and Carpenter (2000, Cladistics 16:298–318) criticize the philosophical foundations of the PhyloCode. They argue that species and higher taxa are not individuals, and they reject the view that taxon names are rigid designators. Furthermore, they charge supporters of the individuality thesis and rigid designator theory with assuming essentialism, committing logical inconsistencies, and offering proposals that render (...) taxonomy untestable. These charges are unsound. Such charges turn on confusions over rigid designator theory and the distinction between kinds and individuals. In addition, Rieppel’s, Keller et al.’s, and Nixon and Carpenter’s proposed alternatives are no better and have their own problems. The individuality thesis and rigid designator theory should not be quickly abandoned. [Individuals; kinds; PhyloCode; rigid designators; species; taxa; taxon names.]. (shrink)

James Valentine's "On the Origin of Phyla" is divided into three main sections: "Evidence of the Origins of Metazoan Phyla," "The Metazoan Phyla," and "The Evolution of the Phyla." The second section is the zoological core of the book, a more or less conventional treatment of major animal taxa, arranged in chain-of-being fashion from sponges to cnidarians to "worms" of many kinds, and so onward to arthropods, echinoderms, chordates, and all others in between. Philosophically inclined readers will be most interested (...) in the first and third sections of the volume, which treat phylogenetic principles and macroevolution respectively. These sections are rich in detail, but Valentine adopts something of a rear-guard position on many issues, arguing in favor of a number of concepts that most systematists have now abandoned. The publisher's advertisement describes "On the Origin of Phyla" as "one of the classic scientific texts of the twentieth century," and for us in the 21st century, that may be the best way to regard it. It will be of greatest value to zoologists who want a good compendium of current comparative data, and to historians and philosophers of science who have an interest in the complex development of phylogenetic "tree-thinking" in systematic biology. (shrink)

Speciation is an aspect of evolutionary biology that has received little philosophical attention apart from articles mainly by biologists such as Mayr (1988). The role of speciation as a terminus a quo for the individuality of species or in the context of punctuated equilibrium theory has been discussed, but not the nature of speciation events themselves. It is the task of this paper to attempt to bring speciation events into some kind of general scheme, based primarily upon the work of (...) Sergey Gavrilets on adaptive landscapes, using migration rate, or gene flow, as the primary scale, and concluding that adaptive and drift explanations are complementary rather than competing. I propose a distinction between intrinsic and extrinsic selection, and the notion of reproductive reach and argue that speciation modes should be discriminated in terms of gene flow, the nature of selection maintaining reproductive reach, and whether the predominant cause is selective or stochastic. I also suggest that the notion of an adaptive “quasispecies” for asexual species is the primitive notion of species, and that members of reproductively coherent sexual species are additionally coadapted to their mating partners. (shrink)

Homeostatic Property Cluster (HPC) theory suggests that species and other biological taxa consist of organisms that share certain similarities. HPC theory acknowledges the existence of Darwinian variation within biological taxa. The claim is that “homeostatic mechanisms” acting on the members of such taxa nonetheless ensure a significant cluster of similarities. The HPC theorist’s focus on individual similarities is inadequate to account for stable polymorphism within taxa, and fails properly to capture their historical nature. A better approach is to treat distributions (...) of traits in species populations as irreducible facts, explained in terms of selection pressures, genealogy, and other evolutionary factors. We call this view Population Structure Theory (PST). PST accommodates the view, implicit in biological systematics, that species are identified by reference to particular historical populations. (shrink)

Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested (...) under highly standardized conditions. Although the number of described prokaryotic species is underrepresented in the living world, this phylo-phenetic or polythetic species concept currently in use is considered to be pragmatic, operational and universally applicable and successfully used for identification processes. (shrink)

Ontological questions in biology have typically focused on the nature of species: what are species; how are they identified and individuated? There is an analogous, but much neglected concern: what are characters; how are they identified and individuated? Character individuation is significant because biological systematics relies on a parsimony principle to determine phylogeny and classify taxa, and the parsimony principle is usually interpreted to favor the phylogenetic hypothesis that requires the fewest changes in characters. But no character individuation principle identified (...) so far is adequate. For biological systematics we need a better way of conceiving characters. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

Advocates of cladistic parsimony methods have invoked the philosophy of Karl Popper in an attempt to argue for the superiority of those methods over phylogenetic methods based on Ronald Fisher's statistical principle of likelihood. We argue that the concept of likelihood in general, and its application to problems of phylogenetic inference in particular, are highly compatible with Popper's philosophy. Examination of Popper's writings reveals that his concept of corroboration is, in fact, based on likelihood. Moreover, because probabilistic assumptions are necessary (...) for calculating the probabilities that define Popper's corroboration, likelihood methods of phylogenetic inference—with their explicit probabilistic basis—are easily reconciled with his concept. In contrast, cladistic parsimony methods, at least as described by certain advocates of those methods, are less easily reconciled with Popper's concept of corroboration. If those methods are interpreted as lacking probabilistic assumptions, then they are incompatible with corroboration. Conversely, if parsimony methods are to be considered compatible with corroboration, then they must be interpreted as carrying implicit probabilistic assumptions. Thus, the non-probabilistic interpretation of cladistic parsimony favored by some advocates of those methods is contradicted by an attempt by the same authors to justify parsimony methods in terms of Popper's concept of corroboration. In addition to being compatible with Popperian corroboration, the likelihood approach to phylogenetic inference permits researchers to test the assumptions of their analytical methods (models) in a way that is consistent with Popper's ideas about the provisional nature of background knowledge. (shrink)

The vast majority of biological taxonomists use the Linnaean system when constructing classifications. Taxa are assigned Linnaean ranks and taxon names are devised according to the Linnaean rules of nomenclature. Unfortunately, the Linnaean system has become theoretically outdated. Moreover, its continued use causes a number of practical problems. This paper begins by sketching the ontological and practical problems facing the Linnaean system. Those problems are sufficiently pressing that alternative systems of classification should be investigated. A number of proposals for an (...) alternative system are introduced and evaluated. The best aspects of those proposals are brought together to form a post-Linnaean system, and a comparison of the Linnaean and post-Linnaean systems is conducted. The final section of this paper considers not only the theoretical reasons for replacing the Linnaean system, but also the practical feasibility of adopting an alternative system. (shrink)

Species serve as both the basic units of macroevolutionary studies and as the basic units of taxonomic classification. In this paper I argue that the taxa identified as species by the Phylogenetic Species Concept (Mishler and Brandon 1987) are the units of biological organization most causally relevant to the evolutionary process but that such units exist at multiple levels within the hierarchy of any phylogenetic lineage. The PSC gives us no way of identifying one of these levels as the privileged (...) level on which taxonomic classifications can be based. (shrink)

Two new modes of thinking have spread through systematics in the twentieth century. Both have deep historical roots, but they have been widely accepted only during this century. Population thinking overtook the field in the early part of the century, culminating in the full development of population systematics in the 1930s and 1940s, and the subsequent growth of the entire field of population biology. Population thinking rejects the idea that each species has a natural type (as the earlier essentialist view (...) had assumed), and instead sees every species as a varying population of interbreeding individuals. Tree thinking has spread through the field since the 1960s with the development of phylogenetic systematics. Tree thinking recognizes that species are not independent replicates within a class (as earlier group thinkers had tended to see them), but are instead interconnected parts of an evolutionary tree. It lays emphasis on the explanation of evolutionary events in the context of a tree, rather than on the states exhibited by collections of species, and it sees evolutionary history as a story of divergence rather than a story of development. Just as population thinking gave rise to the new field of population biology, so tree thinking is giving rise to the new field of phylogenetic biology. (shrink)

Most biologists use the Linnaean system for constructing classifications of the organic world. The Linnaean system, however, has lost its theoretical basis due to the shift in biology from creationist and essentialist tenets to evolutionary theory. As a result, the Linnaean system is both cumbersome and ontologically vacuous. This paper illustrates the problems facing the Linnaean system, and ends with a brief introduction to an alternative approach to biological classification.